Related papers: A concise introduction to molecular dynamics simul…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
Computer simulation of the time evolution in a classical system is a standard numerical method, used in numerous scientific articles in Natural Science. Almost all the simulations are performed by discrete Molecular Dynamics (MD). The…
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
We present a new approach for the two-temperature molecular dynamics (MD) model for coupled simulations of electronic and phonon heat conduction in nanoscale systems. The proposed method uses a master equation to perform heat conduction of…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…
We present OpenMM-Python-Force, a plugin designed to extend OpenMM's functionality by enabling integration of energy and force calculations from external Python programs via a callback mechanism. During molecular dynamics simulations, data…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…
Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
Folding protein dynamics has been an area of high interest for quite some time, especially given the increased focus on the field of Biophysics. Because folding dynamics occur on such short time scales, empirical techniques developed for…
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…
We demonstrate a new method of simulation of nonstationary quantum processes, considering the tunneling of two {\it interacting identical particles}, represented by wave packets. The used method of quantum molecular dynamics (WMD) is based…
We demonstrate that for a broad class of physical systems that can be described using classical field theory, automated runtime translation of the physical equations to parallelized finite-element numerical simulation code is feasible. This…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
Molecular dynamics (MD) simulation, which is considered an important tool for studying physical and chemical processes at the atomic scale, requires accurate calculations of energies and forces. Although reliable energies and forces can be…
We present an open-source, performant, pure-python molecular dynamics (MD) suite for non-ideal plasmas. The code, Sarkas, aims to accelerate the research process by providing an MD code but also pre- and post-processing tools. Sarkas offers…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Multiparticle collision dynamics (MPCD) is a relatively new algorithm of fluid flow simulations that has been applied mostly to flows around simple objects. One might ask how it behaves in more complex flows. Therefore, we extend MPCD to…